Entering edit mode
2.4 years ago
tthung
•
0
Is it possible to calculate fpkm if only log2 fold change and p-values are provided?
1
Entering edit mode
2.4 years ago
Michael
54k
I think not. The explanation is simple, disregarding some additional magic to the log fold change like shrinkage, a fold change is essentially a fraction. Say you are given the following information: x/y = 2, what are x and y? Ofc we can't tell, the p-value doesn't help here either.
Similar Posts
Loading Similar Posts
Traffic: 2369 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6
Oh I see. Then I would like to ask how to find the top 100 unregulated genes in R programming ? Cause I would like only calculate the fpkm of a particular genes which is within the top 100 unregulated genes. By finding the top 100 unregulated genes, I can calculate the total number of mapped reads. Then I could calculate fpkm.
Just to make sure I understand, "unregulated", as in not differentially expressed? Or up-regulated?
oh it's upregulated sorry for the spelling error
If you got logFC and p-values (are these adjusted p-values?) you have everything you need. Simply sort all significant genes by logFC (descending or ascending) and pick the top 100. If you could find the original data, that would really help in case you want to do anything more with the data, like plots, clustering, etc.